doppelgangR

DOI: 10.18129/B9.bioc.doppelgangR  

Identify likely duplicate samples from genomic or meta-data

Bioconductor version: Release (3.16)

The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).

Author: Levi Waldron [aut, cre], Markus Reister [aut, ctb], Marcel Ramos [ctb]

Maintainer: Levi Waldron <lwaldron.research at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("doppelgangR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("doppelgangR")

 

HTML	R Script	doppelgangR vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, ImmunoOncology, Microarray, QualityControl, RNASeq, Software
Version	1.26.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 years)
License	GPL (>=2.0)
Depends	R (>= 3.5.0), Biobase, BiocParallel
Imports	sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat
SystemRequirements
Enhances
URL	https://github.com/lwaldron/doppelgangR
BugReports	https://github.com/lwaldron/doppelgangR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	doppelgangR_1.26.0.tar.gz
Windows Binary	doppelgangR_1.26.0.zip
macOS Binary (x86_64)	doppelgangR_1.26.0.tgz
macOS Binary (arm64)	doppelgangR_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/doppelgangR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/doppelgangR
Bioc Package Browser	https://code.bioconductor.org/browse/doppelgangR/
Package Short Url	https://bioconductor.org/packages/doppelgangR/
Package Downloads Report	Download Stats